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Conserved domains on  [gi|1386813839]
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Chain F, Pachytene checkpoint protein 2 homolog

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RecA-like_Pch2-like cd19508
ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as ...
 121-319 8.15e-134

ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as Thyroid hormone receptor interactor 13 (TRIP13) and 16E1BP) is a key regulator of specific chromosomal events, like the control of G2/prophase processes such as DNA break formation and recombination, checkpoint signaling, and chromosome synapsis. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion


:

Pssm-ID: 410916 [Multi-domain]  Cd Length: 199  Bit Score: 382.56  E-value: 8.15e-134
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 121 AANHWVLPAAEFHGLWDSLVYDVEVKSHLLDYVMTTLLFSDKNVNSNLITWNRVVLLHGPPGTGKTSLCKALAQKLTIRL 200
Cdd:cd19508     1 AANHWLLPAAEFHGLWESLIYDSNLKSRLLDYVTTTLLFSDKNVNTNLITWNRLVLLHGPPGTGKTSLCKALAQKLSIRL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 201 SSRYRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQDLIDDKDALVFVLIDQVESLTAARNACRAGTEPSDAIRVVNAV 280
Cdd:cd19508    81 SSRYRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQELIDDKDALVFVLIDEVESLAAARSASSSGTEPSDAIRVVNAV 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1386813839 281 LTQIDQIKRHSNVVILTTSNITEKIDVAFVDRADIKQYI 319
Cdd:cd19508   161 LTQIDRIKRYHNNVILLTSNLLEKIDVAFVDRADIKQYI 199
McrB super family cl34253
5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB ...
 34-205 1.14e-05

5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB [Defense mechanisms];


The actual alignment was detected with superfamily member COG1401:

Pssm-ID: 441011 [Multi-domain]  Cd Length: 477  Bit Score: 47.46  E-value: 1.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839  34 KKEDINLSVRKLLNRHNIVFGDYTWTEFDEPFLTRNVQSVSIIDTELKVKDSQ--PIDLSACTVALHIFQLNEDGPSSEN 111
Cdd:COG1401    79 LLLDLEKVELNEKLALSEAAVAIEELYELEADSEIEAVGLLLELAERSDALEAleRARLLLELADLEERAALETEVLEAL 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 112 LEEETENIIAANHWVLPAAEFHGLWDSLVYDVEVKShLLDYVMTTLLFSDKNVNSNLITWNRV---VLLHGPPGTGKTSL 188
Cdd:COG1401   159 EAELEELLAAPEDLSADALAAELSAAEELYSEDLES-EDDYLKDLLREKFEETLEAFLAALKTkknVILAGPPGTGKTYL 237

                         170
                  ....*....|....*..
gi 1386813839 189 CKALAQKLTIRLSSRYR 205
Cdd:COG1401   238 ARRLAEALGGEDNGRIE 254
 
Name Accession Description Interval E-value
RecA-like_Pch2-like cd19508
ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as ...
 121-319 8.15e-134

ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as Thyroid hormone receptor interactor 13 (TRIP13) and 16E1BP) is a key regulator of specific chromosomal events, like the control of G2/prophase processes such as DNA break formation and recombination, checkpoint signaling, and chromosome synapsis. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion


Pssm-ID: 410916 [Multi-domain]  Cd Length: 199  Bit Score: 382.56  E-value: 8.15e-134
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 121 AANHWVLPAAEFHGLWDSLVYDVEVKSHLLDYVMTTLLFSDKNVNSNLITWNRVVLLHGPPGTGKTSLCKALAQKLTIRL 200
Cdd:cd19508     1 AANHWLLPAAEFHGLWESLIYDSNLKSRLLDYVTTTLLFSDKNVNTNLITWNRLVLLHGPPGTGKTSLCKALAQKLSIRL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 201 SSRYRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQDLIDDKDALVFVLIDQVESLTAARNACRAGTEPSDAIRVVNAV 280
Cdd:cd19508    81 SSRYRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQELIDDKDALVFVLIDEVESLAAARSASSSGTEPSDAIRVVNAV 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1386813839 281 LTQIDQIKRHSNVVILTTSNITEKIDVAFVDRADIKQYI 319
Cdd:cd19508   161 LTQIDRIKRYHNNVILLTSNLLEKIDVAFVDRADIKQYI 199
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 175-320 2.02e-29

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 111.15  E-value: 2.02e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTIRlssryrygqLIEINSHSLFSKWFSESGKLVTKMFQKIQdliddKDALVFVLIDQV 254
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAP---------FIEISGSELVSKYVGESEKRLRELFEAAK-----KLAPCVIFIDEI 66

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1386813839 255 ESLTAARNacraGTEPSDAIRVVNAVLTQIDQIK-RHSNVVILTTSNITEKIDVAFVDRADIKQYIG 320
Cdd:pfam00004  67 DALAGSRG----SGGDSESRRVVNQLLTELDGFTsSNSKVIVIAATNRPDKLDPALLGRFDRIIEFP 129
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 135-414 1.35e-26

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 110.39  E-value: 1.35e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 135 LWDSLVYDVEVKSHLLDYVMTTLLFSDKNVNSNLiTWNRVVLLHGPPGTGKTSLCKALAQKLTirlssryryGQLIEINS 214
Cdd:COG0464   155 ILDDLGGLEEVKEELRELVALPLKRPELREEYGL-PPPRGLLLYGPPGTGKTLLARALAGELG---------LPLIEVDL 224

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 215 HSLFSKWFSESGKLVTKMFQKIQDLiddkdALVFVLIDQVESLTAARNACRAGTepsdAIRVVNAVLTQIDQIKRHSnVV 294
Cdd:COG0464   225 SDLVSKYVGETEKNLREVFDKARGL-----APCVLFIDEADALAGKRGEVGDGV----GRRVVNTLLTEMEELRSDV-VV 294

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 295 ILTTSNItEKIDVAFVDRADIKQYIGPPSAA---AIFKIYLscleelmkcqiiyPRQQLltlrelemigfiennvsKLSL 371
Cdd:COG0464   295 IAATNRP-DLLDPALLRRFDEIIFFPLPDAEerlEIFRIHL-------------RKRPL-----------------DEDV 343

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1386813839 372 LLNDISRKSEGLSGRVLRKLPFLA--HALYVQAPTVTIEGFLQAL 414
Cdd:COG0464   344 DLEELAEATEGLSGADIRNVVRRAalQALRLGREPVTTEDLLEAL 388
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 169-331 2.63e-17

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 84.19  E-value: 2.63e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 169 ITWNRVVLLHGPPGTGKTSLCKALAQKltirlssryRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQdliddKDALVF 248
Cdd:TIGR01243 484 IRPPKGVLLFGPPGTGKTLLAKAVATE---------SGANFIAVRGPEILSKWVGESEKAIREIFRKAR-----QAAPAI 549

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 249 VLIDQVESLTAARNAcRAGTEPSDaiRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVAFV--DRADIKQYIGPPSAAA 326
Cdd:TIGR01243 550 IFFDEIDAIAPARGA-RFDTSVTD--RIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLrpGRFDRLILVPPPDEEA 626


                  ....*...
gi 1386813839 327 ---IFKIY 331
Cdd:TIGR01243 627 rkeIFKIH 634
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 172-322 4.55e-10

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 57.77  E-value: 4.55e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839  172 NRVVLLHGPPGTGKTSLCKALAQKL--------TIRLSSRYRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQDLIDDk 243
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELgppgggviYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPD- 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1386813839  244 dalvFVLIDQVESLTAARNacragtepSDAIRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVAFVDRADIKQYIGPP 322
Cdd:smart00382  81 ----VLILDEITSLLDAEQ--------EALLLLLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRRRFDRRIVLLLI 147
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 175-333 4.87e-08

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 54.78  E-value: 4.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTirlssryryGQLIEINSHSLFSKWFSESGKLVTKMFQkiqdlIDDKDALVFVLIDQV 254
Cdd:PTZ00361  220 VILYGPPGTGKTLLAKAVANETS---------ATFLRVVGSELIQKYLGDGPKLVRELFR-----VAEENAPSIVFIDEI 285

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 255 ESLTAARNACRAGTEpSDAIRVVNAVLTQIDQIKRHSNV-VILTTSNItEKIDVAFVDRADIKQYIGPP-----SAAAIF 328
Cdd:PTZ00361  286 DAIGTKRYDATSGGE-KEIQRTMLELLNQLDGFDSRGDVkVIMATNRI-ESLDPALIRPGRIDRKIEFPnpdekTKRRIF 363


                  ....*
gi 1386813839 329 KIYLS 333
Cdd:PTZ00361  364 EIHTS 368
McrB COG1401
5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB ...
 34-205 1.14e-05

5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB [Defense mechanisms];


Pssm-ID: 441011 [Multi-domain]  Cd Length: 477  Bit Score: 47.46  E-value: 1.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839  34 KKEDINLSVRKLLNRHNIVFGDYTWTEFDEPFLTRNVQSVSIIDTELKVKDSQ--PIDLSACTVALHIFQLNEDGPSSEN 111
Cdd:COG1401    79 LLLDLEKVELNEKLALSEAAVAIEELYELEADSEIEAVGLLLELAERSDALEAleRARLLLELADLEERAALETEVLEAL 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 112 LEEETENIIAANHWVLPAAEFHGLWDSLVYDVEVKShLLDYVMTTLLFSDKNVNSNLITWNRV---VLLHGPPGTGKTSL 188
Cdd:COG1401   159 EAELEELLAAPEDLSADALAAELSAAEELYSEDLES-EDDYLKDLLREKFEETLEAFLAALKTkknVILAGPPGTGKTYL 237

                         170
                  ....*....|....*..
gi 1386813839 189 CKALAQKLTIRLSSRYR 205
Cdd:COG1401   238 ARRLAEALGGEDNGRIE 254
 
Name Accession Description Interval E-value
RecA-like_Pch2-like cd19508
ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as ...
 121-319 8.15e-134

ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as Thyroid hormone receptor interactor 13 (TRIP13) and 16E1BP) is a key regulator of specific chromosomal events, like the control of G2/prophase processes such as DNA break formation and recombination, checkpoint signaling, and chromosome synapsis. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion


Pssm-ID: 410916 [Multi-domain]  Cd Length: 199  Bit Score: 382.56  E-value: 8.15e-134
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 121 AANHWVLPAAEFHGLWDSLVYDVEVKSHLLDYVMTTLLFSDKNVNSNLITWNRVVLLHGPPGTGKTSLCKALAQKLTIRL 200
Cdd:cd19508     1 AANHWLLPAAEFHGLWESLIYDSNLKSRLLDYVTTTLLFSDKNVNTNLITWNRLVLLHGPPGTGKTSLCKALAQKLSIRL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 201 SSRYRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQDLIDDKDALVFVLIDQVESLTAARNACRAGTEPSDAIRVVNAV 280
Cdd:cd19508    81 SSRYRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQELIDDKDALVFVLIDEVESLAAARSASSSGTEPSDAIRVVNAV 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1386813839 281 LTQIDQIKRHSNVVILTTSNITEKIDVAFVDRADIKQYI 319
Cdd:cd19508   161 LTQIDRIKRYHNNVILLTSNLLEKIDVAFVDRADIKQYI 199
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 175-320 2.02e-29

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 111.15  E-value: 2.02e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTIRlssryrygqLIEINSHSLFSKWFSESGKLVTKMFQKIQdliddKDALVFVLIDQV 254
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAP---------FIEISGSELVSKYVGESEKRLRELFEAAK-----KLAPCVIFIDEI 66

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1386813839 255 ESLTAARNacraGTEPSDAIRVVNAVLTQIDQIK-RHSNVVILTTSNITEKIDVAFVDRADIKQYIG 320
Cdd:pfam00004  67 DALAGSRG----SGGDSESRRVVNQLLTELDGFTsSNSKVIVIAATNRPDKLDPALLGRFDRIIEFP 129
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 135-414 1.35e-26

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 110.39  E-value: 1.35e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 135 LWDSLVYDVEVKSHLLDYVMTTLLFSDKNVNSNLiTWNRVVLLHGPPGTGKTSLCKALAQKLTirlssryryGQLIEINS 214
Cdd:COG0464   155 ILDDLGGLEEVKEELRELVALPLKRPELREEYGL-PPPRGLLLYGPPGTGKTLLARALAGELG---------LPLIEVDL 224

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 215 HSLFSKWFSESGKLVTKMFQKIQDLiddkdALVFVLIDQVESLTAARNACRAGTepsdAIRVVNAVLTQIDQIKRHSnVV 294
Cdd:COG0464   225 SDLVSKYVGETEKNLREVFDKARGL-----APCVLFIDEADALAGKRGEVGDGV----GRRVVNTLLTEMEELRSDV-VV 294

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 295 ILTTSNItEKIDVAFVDRADIKQYIGPPSAA---AIFKIYLscleelmkcqiiyPRQQLltlrelemigfiennvsKLSL 371
Cdd:COG0464   295 IAATNRP-DLLDPALLRRFDEIIFFPLPDAEerlEIFRIHL-------------RKRPL-----------------DEDV 343

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1386813839 372 LLNDISRKSEGLSGRVLRKLPFLA--HALYVQAPTVTIEGFLQAL 414
Cdd:COG0464   344 DLEELAEATEGLSGADIRNVVRRAalQALRLGREPVTTEDLLEAL 388
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 175-319 8.62e-25

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 99.66  E-value: 8.62e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTIrlssryrygQLIEINSHSLFSKWFSESGKLVTKMFQKIQDLiddkdALVFVLIDQV 254
Cdd:cd19481    29 ILLYGPPGTGKTLLAKALAGELGL---------PLIVVKLSSLLSKYVGESEKNLRKIFERARRL-----APCILFIDEI 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1386813839 255 ESLTAARnacRAGTEPSDAIRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVAFVD--RADIKQYI 319
Cdd:cd19481    95 DAIGRKR---DSSGESGELRRVLNQLLTELDGVNSRSKVLVIAATNRPDLLDPALLRpgRFDEVIEF 158
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 175-415 8.72e-23

ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 98.15  E-value: 8.72e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTIrlssryrygQLIEINSHSLFSKWFSESGKLVTKMFQKIQdliddKDALVFVLIDQV 254
Cdd:COG1222   115 VLLYGPPGTGKTLLAKAVAGELGA---------PFIRVRGSELVSKYIGEGARNVREVFELAR-----EKAPSIIFIDEI 180

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 255 ESLTAARNAcrAGTepSDAI-RVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVAFV--DRADIKQYIGPPSAAA---IF 328
Cdd:COG1222   181 DAIAARRTD--DGT--SGEVqRTVNQLLAELDGFESRGDVLIIAATNRPDLLDPALLrpGRFDRVIEVPLPDEEAreeIL 256

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 329 KIYLScleelmkcqiiyprqqlltlrelemigfiENNVSKlSLLLNDISRKSEGLSGRVLRKLPFLA--HALYVQAPTVT 406
Cdd:COG1222   257 KIHLR-----------------------------DMPLAD-DVDLDKLAKLTEGFSGADLKAIVTEAgmFAIREGRDTVT 306


                  ....*....
gi 1386813839 407 IEGFLQALS 415
Cdd:COG1222   307 MEDLEKAIE 315
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
173-427 1.22e-20

Predicted ATPase, AAA+ superfamily [General function prediction only];


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 90.33  E-value: 1.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 173 RVVLLHGPPGTGKTSLCKALAQKLTIRlssryrygqLIEINSHSLFSKWFSESGKLVTKMFqkiqDLIDDKDALVFvlID 252
Cdd:COG1223    36 RKILFYGPPGTGKTMLAEALAGELKLP---------LLTVRLDSLIGSYLGETARNLRKLF----DFARRAPCVIF--FD 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 253 QVESLTAARnacRAGTEPSDAIRVVNAVLTQIDQIKrhSNVVILTTSNITEKIDVAFVDRADIKQYIGPPSAAAIFKIYL 332
Cdd:COG1223   101 EFDAIAKDR---GDQNDVGEVKRVVNALLQELDGLP--SGSVVIAATNHPELLDSALWRRFDEVIEFPLPDKEERKEILE 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 333 SCLEELmkcqiiyprqqlltlrelemigfiennVSKLSLLLNDISRKSEGLSGRVLRKL--PFLAHALYVQAPTVTIEGF 410
Cdd:COG1223   176 LNLKKF---------------------------PLPFELDLKKLAKKLEGLSGADIEKVlkTALKKAILEDREKVTKEDL 228

                         250
                  ....*....|....*..
gi 1386813839 411 LQALSLAVDKQFEERKK 427
Cdd:COG1223   229 EEALKQRKERKKEPKKE 245
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 169-308 5.85e-20

first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. This subfamily also includes the first of the two ATPase domains of NVL (nuclear VCP-like protein) 2, an isoform of NVL mainly present in the nucleolus, which is involved in ribosome biogenesis, in telomerase assembly and the regulation of telomerase activity, and in pre-rRNA processing. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410911 [Multi-domain]  Cd Length: 165  Bit Score: 86.58  E-value: 5.85e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 169 ITWNRVVLLHGPPGTGKTSLCKALAQKLTIrlssryrygQLIEINSHSLFSKWFSESGKLVTKMFQKIQDLiddKDALVF 248
Cdd:cd19503    31 LKPPRGVLLHGPPGTGKTLLARAVANEAGA---------NFLSISGPSIVSKYLGESEKNLREIFEEARSH---APSIIF 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 249 vlIDQVESLTAARNACRAGTEpsdaIRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVA 308
Cdd:cd19503    99 --IDEIDALAPKREEDQREVE----RRVVAQLLTLMDGMSSRGKVVVIAATNRPDAIDPA 152
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 144-319 7.37e-19

ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This subfamily includes the ATPase domains of vacuolar protein sorting-associated protein 4 (VPS4), ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase), Katanin p60 ATPase-containing subunit A1 (KTNA1), Spastin, and Fidgetin-Like 1 (FIGL-1). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410917 [Multi-domain]  Cd Length: 163  Bit Score: 83.17  E-value: 7.37e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 144 EVKSHLLDYVMTTLLFSDknVNSNLITWNRVVLLHGPPGTGKTSLCKALAQKLTirlssryryGQLIEINSHSLFSKWFS 223
Cdd:cd19509     6 DAKEALKEAVILPSLRPD--LFPGLRGPPRGILLYGPPGTGKTLLARAVASESG---------STFFSISASSLVSKWVG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 224 ESGKLVTKMFQKIQDLiddKDALVFvlIDQVESLTAARNAcragTEPSDAIRVVNAVLTQIDQIKRHSN--VVILTTSNI 301
Cdd:cd19509    75 ESEKIVRALFALAREL---QPSIIF--IDEIDSLLSERGS----GEHEASRRVKTEFLVQMDGVLNKPEdrVLVLGATNR 145

                         170
                  ....*....|....*...
gi 1386813839 302 TEKIDVAFVDRADIKQYI 319
Cdd:cd19509   146 PWELDEAFLRRFEKRIYI 163
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 175-308 4.72e-18

second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase domains; This subfamily includes the second of two ATPase domains of the molecular chaperone CDC48 in yeast and p97 or VCP in metazoans, Peroxisomal biogenesis factor 1 (PEX1) and -6 (PEX6), Valosin-containing protein-like ATPase (VAT), and nuclear VCP-like protein (NVL). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410919 [Multi-domain]  Cd Length: 159  Bit Score: 80.79  E-value: 4.72e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTIrlssryrygQLIEINSHSLFSKWFSESGKLVTKMFQKIQdliDDKDALVFvlIDQV 254
Cdd:cd19511    30 VLLYGPPGCGKTLLAKALASEAGL---------NFISVKGPELFSKYVGESERAVREIFQKAR---QAAPCIIF--FDEI 95

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1386813839 255 ESLTAARNAcRAGTEPSDaiRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVA 308
Cdd:cd19511    96 DSLAPRRGQ-SDSSGVTD--RVVSQLLTELDGIESLKGVVVIAATNRPDMIDPA 146
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 145-319 1.19e-17

second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP in metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the second of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r2-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410936 [Multi-domain]  Cd Length: 161  Bit Score: 79.86  E-value: 1.19e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 145 VKSHLLDYVMTTLLFSDKNVNSNLiTWNRVVLLHGPPGTGKTSLCKALAQKLTirlssryryGQLIEINSHSLFSKWFSE 224
Cdd:cd19528     1 VKRELQELVQYPVEHPDKFLKFGM-TPSKGVLFYGPPGCGKTLLAKAIANECQ---------ANFISVKGPELLTMWFGE 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 225 SGKLVTKMFQKIQdliddKDALVFVLIDQVESLTAARNAcRAGTEPSDAIRVVNAVLTQIDQIKRHSNVVILTTSNITEK 304
Cdd:cd19528    71 SEANVRDIFDKAR-----AAAPCVLFFDELDSIAKARGG-NIGDAGGAADRVINQILTEMDGMNTKKNVFIIGATNRPDI 144

                         170
                  ....*....|....*
gi 1386813839 305 IDVAFVDRADIKQYI 319
Cdd:cd19528   145 IDPAILRPGRLDQLI 159
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 169-331 2.63e-17

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 84.19  E-value: 2.63e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 169 ITWNRVVLLHGPPGTGKTSLCKALAQKltirlssryRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQdliddKDALVF 248
Cdd:TIGR01243 484 IRPPKGVLLFGPPGTGKTLLAKAVATE---------SGANFIAVRGPEILSKWVGESEKAIREIFRKAR-----QAAPAI 549

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 249 VLIDQVESLTAARNAcRAGTEPSDaiRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVAFV--DRADIKQYIGPPSAAA 326
Cdd:TIGR01243 550 IFFDEIDAIAPARGA-RFDTSVTD--RIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLrpGRFDRLILVPPPDEEA 626


                  ....*...
gi 1386813839 327 ---IFKIY 331
Cdd:TIGR01243 627 rkeIFKIH 634
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 145-310 8.56e-16

second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ATPase domains; The Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), is an archaeal homolog of the ubiquitous Cdc48/p97. It is a protein unfoldase that functions in concert with the 20S proteasome by unfolding proteasome substrates and passing them on for degradation. VAT forms a homohexamer, each monomer contains two tandem ATPase domains, referred to as D1 and D2, and an N-terminal domain. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410937 [Multi-domain]  Cd Length: 159  Bit Score: 74.45  E-value: 8.56e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 145 VKSHLLDYVMTTLLFSDKNVNSNlITWNRVVLLHGPPGTGKTSLCKALAQKltirlsSRYRYgqlIEINSHSLFSKWFSE 224
Cdd:cd19529     1 VKQELKEAVEWPLLKPEVFKRLG-IRPPKGILLYGPPGTGKTLLAKAVATE------SNANF---ISVKGPELLSKWVGE 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 225 SGKLVTKMFQKIQDLiddkdALVFVLIDQVESLtaarnACRAGTEPSDAI--RVVNAVLTQIDQIKRHSNVVILTTSNIT 302
Cdd:cd19529    71 SEKAIREIFRKARQV-----APCVIFFDEIDSI-----APRRGTTGDSGVteRVVNQLLTELDGLEEMNGVVVIAATNRP 140


                  ....*...
gi 1386813839 303 EKIDVAFV 310
Cdd:cd19529   141 DIIDPALL 148
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 144-312 3.95e-15

ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase) is an ATPase that plays a critical role in regulating the surface expression of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, thereby regulating synaptic plasticity, learning and memory. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410928 [Multi-domain]  Cd Length: 166  Bit Score: 72.84  E-value: 3.95e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 144 EVKSHLLDYVMTTLLFSDKNVNSNLITWNRVVLLHGPPGTGKTSLCKALAQKLTIRlssryrygqLIEINSHSLFSKWFS 223
Cdd:cd19520     7 EVITELKELVILPLQRPELFDNSRLLQPPKGVLLYGPPGCGKTMLAKATAKEAGAR---------FINLQVSSLTDKWYG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 224 ESGKLVTKMF---QKIQDLIddkdalvfVLIDQVESLTAARNacragtePSD--AIRVVNA-VLTQIDQI--KRHSNVVI 295
Cdd:cd19520    78 ESQKLVAAVFslaSKLQPSI--------IFIDEIDSFLRQRS-------STDheATAMMKAeFMSLWDGLstDGNCRVIV 142

                         170
                  ....*....|....*..
gi 1386813839 296 LTTSNITEKIDVAFVDR 312
Cdd:cd19520   143 MGATNRPQDLDEAILRR 159
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
 168-319 2.07e-14

ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein sorting-associated protein 4 (Vps4) is believed to be involved in intracellular protein transport out of a prevacuolar endosomal compartment. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410929 [Multi-domain]  Cd Length: 170  Bit Score: 70.66  E-value: 2.07e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 168 LITWNRV----VLLHGPPGTGKTSLCKALAQKLTIRLSSryrygqlieINSHSLFSKWFSESGKLVTKMFQKIQdliDDK 243
Cdd:cd19521    32 LFTGNRKpwsgILLYGPPGTGKSYLAKAVATEANSTFFS---------VSSSDLVSKWMGESEKLVKQLFAMAR---ENK 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1386813839 244 DALVFvlIDQVESLTAARNAcragTEPSDAIRVVNAVLTQIDQIKRHSN-VVILTTSNITEKIDVAFVDRADIKQYI 319
Cdd:cd19521   100 PSIIF--IDEVDSLCGTRGE----GESEASRRIKTELLVQMNGVGNDSQgVLVLGATNIPWQLDSAIRRRFEKRIYI 170
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 173-308 1.76e-13

first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r1-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410927 [Multi-domain]  Cd Length: 166  Bit Score: 68.23  E-value: 1.76e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 173 RVVLLHGPPGTGKTSLCKALAQKltirlSSRYrygqLIEINSHSLFSKWFSESGKLVTKMFQKIQdliddKDALVFVLID 252
Cdd:cd19519    35 RGILLYGPPGTGKTLIARAVANE-----TGAF----FFLINGPEIMSKLAGESESNLRKAFEEAE-----KNAPAIIFID 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1386813839 253 QVESLTAARNACRAGTEPsdaiRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVA 308
Cdd:cd19519   101 EIDAIAPKREKTHGEVER----RIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPA 152
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 175-309 7.94e-12

second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL exists in two forms with N-terminal extensions of different lengths in mammalian cells. NVL has two alternatively spliced isoforms, a short form, NVL1, and a long form, NVL2. NVL2, the major species, is mainly present in the nucleolus, whereas NVL1 is nucleoplasmic. Each has an N-terminal domain, followed by two tandem ATPase domains; this subfamily includes the first of the two ATPase domains. NVL2 is involved in the biogenesis of the 60S ribosome subunit by associating specifically with ribosome protein L5 and modulating the function of DOB1. NVL2 is also required for telomerase assembly and the regulation of telomerase activity, and is involved in pre-rRNA processing. The role of NVL1 is unclear. This RecA-like_NVL_r1-like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410938 [Multi-domain]  Cd Length: 161  Bit Score: 63.28  E-value: 7.94e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTIrlssryrygQLIEINSHSLFSKWFSESGKLVTKMFQKIQDliddkDALVFVLIDQV 254
Cdd:cd19530    33 VLLYGPPGCGKTLLAKAVANESGA---------NFISVKGPELLNKYVGESERAVRQVFQRARA-----SAPCVIFFDEV 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1386813839 255 ESLTAARNacraGTEPSDAIRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVAF 309
Cdd:cd19530    99 DALVPKRG----DGGSWASERVVNQLLTEMDGLEERSNVFVIAATNRPDIIDPAM 149
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 175-322 2.12e-11

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 66.08  E-value: 2.12e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTirlssryryGQLIEINSHSLFSKWFSESGKLVTKMFQKIQDliddkDALVFVLIDQV 254
Cdd:TIGR01243 215 VLLYGPPGTGKTLLAKAVANEAG---------AYFISINGPEIMSKYYGESEERLREIFKEAEE-----NAPSIIFIDEI 280

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 255 ESLTAARNACRAGTEPsdaiRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVAF--VDRADIKQYIGPP 322
Cdd:TIGR01243 281 DAIAPKREEVTGEVEK----RVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALrrPGRFDREIVIRVP 346
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
 175-319 3.49e-11

Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is the catalytic subunit of the Katanin complex which is severs microtubules in an ATP-dependent manner, and is implicated in multiple aspects of microtubule dynamics. In addition to the p60 catalytic ATPase subunit, Katanin contains an accessory subunit (p80 or p80-like). The microtubule-severing activity of the ATPase is essential for female meiotic spindle assembly, and male gamete production; and the katanin complex severing microtubules is under tight regulation during the transition from the meiotic to mitotic stage to allow proper embryogenesis. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410930 [Multi-domain]  Cd Length: 170  Bit Score: 61.54  E-value: 3.49e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTIrlssryrygQLIEINSHSLFSKWFSESGKLVTKMFQKIQDLiddkdALVFVLIDQV 254
Cdd:cd19522    36 VLMVGPPGTGKTLLAKAVATECGT---------TFFNVSSSTLTSKYRGESEKLVRLLFEMARFY-----APTTIFIDEI 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1386813839 255 ESLTAARNacrAGTEPSDAIRVVNAVLTQIDQIKRHSN-------VVILTTSNITEKIDVAFVDRADIKQYI 319
Cdd:cd19522   102 DSICSRRG---TSEEHEASRRVKSELLVQMDGVGGASEnddpskmVMVLAATNFPWDIDEALRRRLEKRIYI 170
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 175-321 4.50e-11

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 60.62  E-value: 4.50e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLtirlssRYRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQDLidDKDALVFVLIDQV 254
Cdd:cd00009    22 LLLYGPPGTGKTTLARAIANEL------FRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELA--EKAKPGVLFIDEI 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1386813839 255 ESLTAARNAcragtepsdaiRVVNAVLTQIDQIKRHSNV-VILTTSNITE-KIDVAFVDRADIKQYIGP 321
Cdd:cd00009    94 DSLSRGAQN-----------ALLRVLETLNDLRIDRENVrVIGATNRPLLgDLDRALYDRLDIRIVIPL 151
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 175-308 4.15e-10

proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily contains ATPase subunits of the eukaryotic 26S proteasome, and of the archaeal proteasome which carry out ATP-dependent degradation of substrates of the ubiquitin-proteasome pathway. The eukaryotic 26S proteasome consists of a proteolytic 20S core particle (CP), and a 19S regulatory particle (RP) which provides the ATP-dependence and the specificity for ubiquitinated proteins. In the archaea the RP is a homohexameric complex of proteasome-activating nucleotidase (PAN). This subfamily also includes various eukaryotic 26S subunits including, proteasome 26S subunit, ATPase 2 (PSMC2, also known as S7 and MSS1) which is a member of the 19S RP and has a chaperone like activity; and proteasome 20S subunit alpha 6 (PSMA6, also known as IOTA, p27K, and PROS27) which is a member of the 20S CP. This RecA-like_PAN subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410910 [Multi-domain]  Cd Length: 171  Bit Score: 58.50  E-value: 4.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTirlssryryGQLIEINSHSLFSKWFSESGKLVTKMFQkiqdLIDDKDALVfVLIDQV 254
Cdd:cd19502    40 VLLYGPPGTGKTLLAKAVANHTD---------ATFIRVVGSELVQKYIGEGARLVRELFE----MAREKAPSI-IFIDEI 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1386813839 255 ESLTAARNACRAGTEpSDAIRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVA 308
Cdd:cd19502   106 DAIGAKRFDSGTGGD-REVQRTMLELLNQLDGFDPRGNIKVIMATNRPDILDPA 158
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 172-322 4.55e-10

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 57.77  E-value: 4.55e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839  172 NRVVLLHGPPGTGKTSLCKALAQKL--------TIRLSSRYRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQDLIDDk 243
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELgppgggviYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPD- 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1386813839  244 dalvFVLIDQVESLTAARNacragtepSDAIRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVAFVDRADIKQYIGPP 322
Cdd:smart00382  81 ----VLILDEITSLLDAEQ--------EALLLLLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRRRFDRRIVLLLI 147
RecA-like_NSF-SEC18_r1-like cd19504
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ...
 175-310 1.18e-09

first of two ATPase domains of NSF and SEC18, and similar ATPase domains; N-ethylmaleimide-sensitive factor (NSF) and Saccharomyces cerevisiae Vesicular-fusion protein Sec18, key factors for eukaryotic trafficking, are ATPases and SNARE disassembly chaperones. NSF/Sec18 activate or prime SNAREs, the terminal catalysts of membrane fusion. Sec18/NSF associates with SNARE complexes through binding Sec17/alpha-SNAP. Sec18 has an N-terminal cap domain and two nucleotide-binding domains (D1 and D2) which form the two rings of the hexameric complex. The hydrolysis of ATP by D1 generates most of the energy necessary to disassemble inactive SNARE bundles, while the D2 ring binds ATP to stabilize the homohexamer. This subfamily includes the first (D1) ATPase domain of NSF/Sec18, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410912 [Multi-domain]  Cd Length: 177  Bit Score: 57.11  E-value: 1.18e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTIRLSSRyrygqlieINSHSLFSKWFSESGKLVTKMF---QKIQDLIDDKDALVFVLI 251
Cdd:cd19504    38 ILLYGPPGTGKTLMARQIGKMLNAREPKI--------VNGPEILNKYVGESEANIRKLFadaEEEQRRLGANSGLHIIIF 109

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1386813839 252 DQVESLTAARNACRAGTEPSDAirVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVAFV 310
Cdd:cd19504   110 DEIDAICKQRGSMAGSTGVHDT--VVNQLLSKIDGVEQLNNILVIGMTNRKDLIDEALL 166
RecA-like_Figl-1 cd19525
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ...
 175-319 5.59e-09

ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; it may be involved in DNA double-strand break repair via homologous recombination. Caenorhabditis elegans FIGL-1 is a nuclear protein and controls the mitotic progression in the germ line and mouse FIGL-1 may be involved in the control of male meiosis. human FIGL-1 has been shown to be a centrosome protein involved in ciliogenesis perhaps as a microtubule-severing protein. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410933 [Multi-domain]  Cd Length: 186  Bit Score: 55.38  E-value: 5.59e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTirlssryryGQLIEINSHSLFSKWFSESGKLVTKMFQ--KIQdliddKDALVFvlID 252
Cdd:cd19525    58 ILLFGPPGTGKTLIGKCIASQSG---------ATFFSISASSLTSKWVGEGEKMVRALFSvaRCK-----QPAVIF--ID 121

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1386813839 253 QVESLTAArnacRAGTEPSDAIRVVNAVLTQIDQIKRHSN--VVILTTSNITEKIDVAFVDRADIKQYI 319
Cdd:cd19525   122 EIDSLLSQ----RGEGEHESSRRIKTEFLVQLDGATTSSEdrILVVGATNRPQEIDEAARRRLVKRLYI 186
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 175-308 2.01e-08

second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as Peroxin-1)/PEX6 is a protein unfoldase; PEX1 and PEX6 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. PEX-1 is required for stability of PEX5. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410934 [Multi-domain]  Cd Length: 158  Bit Score: 53.20  E-value: 2.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTIRlssryrygqLIEINSHSLFSKWFSESGKLVTKMFQKIQDLiddKDALVFvlIDQV 254
Cdd:cd19526    30 ILLYGPPGCGKTLLASAIASECGLN---------FISVKGPELLNKYIGASEQNVRDLFSRAQSA---KPCILF--FDEF 95

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1386813839 255 ESLTAARNACRAGTepSDaiRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVA 308
Cdd:cd19526    96 DSIAPKRGHDSTGV--TD--RVVNQLLTQLDGVEGLDGVYVLAATSRPDLIDPA 145
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 145-310 2.88e-08

second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as Peroxin61)/PEX1 is a protein unfoldase; PEX6 and PEX1 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. This subfamily represents the second ATPase domain of PEX6. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410935 [Multi-domain]  Cd Length: 160  Bit Score: 52.90  E-value: 2.88e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 145 VKSHLLDYVMTTLLFSDknVNSNLITWNRVVLLHGPPGTGKTSLCKALAQKLTIRLSSryrygqlieINSHSLFSKWFSE 224
Cdd:cd19527     1 VKKEILDTIQLPLEHPE--LFSSGLRKRSGILLYGPPGTGKTLLAKAIATECSLNFLS---------VKGPELINMYIGE 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 225 SGKLVTKMFQKIQDLiddKDALVFvlIDQVESLTAARNacRAGTEPSDAIRVVNAVLTQIDQI-KRHSNVVILTTSNITE 303
Cdd:cd19527    70 SEANVREVFQKARDA---KPCVIF--FDELDSLAPSRG--NSGDSGGVMDRVVSQLLAELDGMsSSGQDVFVIGATNRPD 142


                  ....*..
gi 1386813839 304 KIDVAFV 310
Cdd:cd19527   143 LLDPALL 149
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 173-319 3.49e-08

ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in microtubule dynamics; it specifically recognizes and cuts microtubules that are polyglutamylated. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410932 [Multi-domain]  Cd Length: 164  Bit Score: 52.54  E-value: 3.49e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 173 RVVLLHGPPGTGKTSLCKALAQKLTIrlssryrygQLIEINSHSLFSKWFSESGKLVTKMFQKIQDLiddKDALVFvlID 252
Cdd:cd19524    34 RGLLLFGPPGNGKTMLAKAVAAESNA---------TFFNISAASLTSKYVGEGEKLVRALFAVAREL---QPSIIF--ID 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1386813839 253 QVESLTAARNAcragTEPSDAIRVVNAVLTQIDQIKRHSN--VVILTTSNITEKIDVAFVDRADIKQYI 319
Cdd:cd19524   100 EVDSLLSERSE----GEHEASRRLKTEFLIEFDGVQSNGDdrVLVMGATNRPQELDDAVLRRFTKRVYV 164
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 175-333 4.87e-08

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 54.78  E-value: 4.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTirlssryryGQLIEINSHSLFSKWFSESGKLVTKMFQkiqdlIDDKDALVFVLIDQV 254
Cdd:PTZ00361  220 VILYGPPGTGKTLLAKAVANETS---------ATFLRVVGSELIQKYLGDGPKLVRELFR-----VAEENAPSIVFIDEI 285

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 255 ESLTAARNACRAGTEpSDAIRVVNAVLTQIDQIKRHSNV-VILTTSNItEKIDVAFVDRADIKQYIGPP-----SAAAIF 328
Cdd:PTZ00361  286 DAIGTKRYDATSGGE-KEIQRTMLELLNQLDGFDSRGDVkVIMATNRI-ESLDPALIRPGRIDRKIEFPnpdekTKRRIF 363


                  ....*
gi 1386813839 329 KIYLS 333
Cdd:PTZ00361  364 EIHTS 368
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 173-308 5.02e-08

first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL exists in two forms with N-terminal extensions of different lengths in mammalian cells. NVL has two alternatively spliced isoforms, a short form, NVL1, and a long form, NVL2. NVL2, the major species, is mainly present in the nucleolus, whereas NVL1 is nucleoplasmic. Each has an N-terminal domain, followed by two tandem ATPase domains; this subfamily includes the first of the two ATPase domains. NVL2 is involved in the biogenesis of the 60S ribosome subunit by associating specifically with ribosome protein L5 and modulating the function of DOB1. NVL2 is also required for telomerase assembly and the regulation of telomerase activity, and is involved in pre-rRNA processing. The role of NVL1 is unclear. This RecA-like_NVL_r1-like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410926 [Multi-domain]  Cd Length: 169  Bit Score: 52.41  E-value: 5.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 173 RVVLLHGPPGTGKTSLCKALAQKLTIrlssryrygQLIEINSHSLFSKWFSESGKlvtkmfqKIQDLIDD--KDALVFVL 250
Cdd:cd19518    35 RGVLLHGPPGCGKTMLANAIAGELKV---------PFLKISATEIVSGVSGESEE-------KIRELFDQaiSNAPCIVF 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1386813839 251 IDQVESLTAARNACRAGTEPsdaiRVVNAVLTQIDQIKRHSN----VVILTTSNITEKIDVA 308
Cdd:cd19518    99 IDEIDAITPKRESAQREMER----RIVSQLLTCMDELNNEKTaggpVLVIGATNRPDSLDPA 156
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 175-308 2.53e-07

ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. It is anchored to the cytoplasmic membrane such that the amino- and carboxy-termini are exposed to the cytoplasm. It presents a membrane-bound hexameric structure that is able to unfold and degrade protein substrates. It is comprised of an N-terminal transmembrane region and the larger C-terminal cytoplasmic region, which consists of an ATPase domain and a protease domain. This RecA-Like FTsH subfamily represents the ATPase domain, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410909 [Multi-domain]  Cd Length: 171  Bit Score: 50.31  E-value: 2.53e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKltirlssryrygqlieinSHSLFskwFSESGKLVTKMF-----QKIQDLIDD--KDALV 247
Cdd:cd19501    40 VLLVGPPGTGKTLLAKAVAGE------------------AGVPF---FSISGSDFVEMFvgvgaSRVRDLFEQakKNAPC 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1386813839 248 FVLIDQVESLTAARNACRAGTEPSDAiRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVA 308
Cdd:cd19501    99 IVFIDEIDAVGRKRGAGLGGGHDERE-QTLNQLLVEMDGFESNTGVIVIAATNRPDVLDPA 158
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 149-308 1.05e-06

ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces cerevisiae Yta7 is a chromatin-associated AAA-ATPase involved in regulation of chromatin dynamics. Its human ortholog ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. The RecA-like_Yta7 subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410925 [Multi-domain]  Cd Length: 170  Bit Score: 48.66  E-value: 1.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 149 LLDYVMTTLLFSDKNVNSNlITWNRVVLLHGPPGTGKTSLCKALA-------QKLTIRLssryRYGQlieinshSLFSKW 221
Cdd:cd19517    12 LKEMVFFPLLYPEVFAKFK-ITPPRGVLFHGPPGTGKTLMARALAaecskggQKVSFFM----RKGA-------DCLSKW 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 222 FSESGKLVTKMFQKIQDLiddKDALVFvlIDQVESLTAARNACRAGTEPSdairVVNAVLTQIDQIKRHSNVVILTTSNI 301
Cdd:cd19517    80 VGEAERQLRLLFEEAYRM---QPSIIF--FDEIDGLAPVRSSKQEQIHAS----IVSTLLALMDGLDNRGQVVVIGATNR 150


                  ....*..
gi 1386813839 302 TEKIDVA 308
Cdd:cd19517   151 PDALDPA 157
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
 173-308 1.11e-06

26S protease regulatory subunit 6B-like protein; Provisional


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 50.53  E-value: 1.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 173 RVVLLHGPPGTGKTSLCKALAQKLTirlssryryGQLIEINSHSLFSKWFSESGKLVTKMFQkiqdlIDDKDALVFVLID 252
Cdd:PTZ00454  180 RGVLLYGPPGTGKTMLAKAVAHHTT---------ATFIRVVGSEFVQKYLGEGPRMVRDVFR-----LARENAPSIIFID 245

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1386813839 253 QVESLTAARNACRAGTEpSDAIRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVA 308
Cdd:PTZ00454  246 EVDSIATKRFDAQTGAD-REVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPA 300
AAA_22 pfam13401
AAA domain;
173-260 8.56e-06

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 45.03  E-value: 8.56e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 173 RVVLLHGPPGTGKTSLCKALAQKLTIRLSSRYRY-----GQLIEINsHSLFSKWFSESGKLVTK--MFQKIQDLIDDKDA 245
Cdd:pfam13401   6 GILVLTGESGTGKTTLLRRLLEQLPEVRDSVVFVdlpsgTSPKDLL-RALLRALGLPLSGRLSKeeLLAALQQLLLALAV 84

                          90
                  ....*....|....*
gi 1386813839 246 LVFVLIDQVESLTAA 260
Cdd:pfam13401  85 AVVLIIDEAQHLSLE 99
McrB COG1401
5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB ...
 34-205 1.14e-05

5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB [Defense mechanisms];


Pssm-ID: 441011 [Multi-domain]  Cd Length: 477  Bit Score: 47.46  E-value: 1.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839  34 KKEDINLSVRKLLNRHNIVFGDYTWTEFDEPFLTRNVQSVSIIDTELKVKDSQ--PIDLSACTVALHIFQLNEDGPSSEN 111
Cdd:COG1401    79 LLLDLEKVELNEKLALSEAAVAIEELYELEADSEIEAVGLLLELAERSDALEAleRARLLLELADLEERAALETEVLEAL 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 112 LEEETENIIAANHWVLPAAEFHGLWDSLVYDVEVKShLLDYVMTTLLFSDKNVNSNLITWNRV---VLLHGPPGTGKTSL 188
Cdd:COG1401   159 EAELEELLAAPEDLSADALAAELSAAEELYSEDLES-EDDYLKDLLREKFEETLEAFLAALKTkknVILAGPPGTGKTYL 237

                         170
                  ....*....|....*..
gi 1386813839 189 CKALAQKLTIRLSSRYR 205
Cdd:COG1401   238 ARRLAEALGGEDNGRIE 254
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
175-332 1.17e-05

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 47.72  E-value: 1.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTIrlssryrygqlieinshslfsKWFSESGKLVTKMF-----QKIQDLIDD--KDALV 247
Cdd:PRK10733  188 VLMVGPPGTGKTLLAKAIAGEAKV---------------------PFFTISGSDFVEMFvgvgaSRVRDMFEQakKAAPC 246

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 248 FVLIDQVESLTAARNACRAGTEpSDAIRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVAFV--DRADIKQYIGPPSAA 325
Cdd:PRK10733  247 IIFIDEIDAVGRQRGAGLGGGH-DEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLrpGRFDRQVVVGLPDVR 325

                         170
                  ....*....|
gi 1386813839 326 A---IFKIYL 332
Cdd:PRK10733  326 GreqILKVHM 335
RecA-like_fidgetin cd19523
ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. ...
 145-308 1.24e-05

ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410931 [Multi-domain]  Cd Length: 163  Bit Score: 45.26  E-value: 1.24e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 145 VKSHLLDYVMTTLLFSDknVNSNLITWNRVVLLHGPPGTGKTSLCKALAQKLTirlssryryGQLIEINSHSLFSKWFSE 224
Cdd:cd19523     8 LKAAIKEEVLWPLLRPD--AFSGLLRLPRSILLFGPRGTGKTLLGRCLASQLG---------ATFLRLRGSTLVAKWAGE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 225 SGKLVTKMFqkiqdLIDDKDALVFVLIDQVESLTAARNacrAGTEPSDAIRVvnAVLTQIDQI--KRHSNVVILTTSNIT 302
Cdd:cd19523    77 GEKILQASF-----LAARCRQPSVLFISDLDALLSSQD---DEASPVGRLQV--ELLAQLDGVlgSGEDGVLVVCTTSKP 146


                  ....*.
gi 1386813839 303 EKIDVA 308
Cdd:cd19523   147 EEIDES 152
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
 169-196 5.65e-05

Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of mitochondrial respiratory chain complex III and plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex. RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410918 [Multi-domain]  Cd Length: 153  Bit Score: 43.11  E-value: 5.65e-05
                          10        20
                  ....*....|....*....|....*...
gi 1386813839 169 ITWNRVVLLHGPPGTGKTSLCKALAQKL 196
Cdd:cd19510    20 IPYRRGYLLYGPPGTGKSSFIAALAGEL 47
COG0645 COG0645
Predicted kinase, contains AAA domain [General function prediction only];
174-202 7.63e-05

Predicted kinase, contains AAA domain [General function prediction only];


Pssm-ID: 440410 [Multi-domain]  Cd Length: 164  Bit Score: 42.98  E-value: 7.63e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 1386813839 174 VVLLHGPPGTGKTSLCKALAQKL-TIRLSS 202
Cdd:COG0645     1 LILVCGLPGSGKSTLARALAERLgAVRLRS 30
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 175-193 8.71e-05

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 44.44  E-value: 8.71e-05
                          10
                  ....*....|....*....
gi 1386813839 175 VLLHGPPGTGKTSLCKALA 193
Cdd:PRK03992  168 VLLYGPPGTGKTLLAKAVA 186
RecA-like_ATAD3-like cd19512
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ...
 173-314 1.51e-04

ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase domains; ATPase AAA-domain protein 3 (ATAD3) is a ubiquitously expressed mitochondrial protein involved in mitochondrial dynamics, DNA-nucleoid structural organization, cholesterol transport and steroidogenesis. The ATAD3 gene family in human comprises three paralog genes: ATAD3A, ATAD3B and ATAD3C. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410920 [Multi-domain]  Cd Length: 150  Bit Score: 41.74  E-value: 1.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 173 RVVLLHGPPGTGKTSLCKALAQKltirlsSRYRYGQLIEINSHSLfskwfseSGKLVTKMfQKIQDLIDDKDALVFVLID 252
Cdd:cd19512    23 RNILFYGPPGTGKTLFAKKLALH------SGMDYAIMTGGDVAPM-------GREGVTAI-HKVFDWANTSRRGLLLFVD 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1386813839 253 QVESLTAARNAcragTEPSDAIR-VVNAVLTQIDQikrHSN-VVILTTSNITEKIDVAFVDRAD 314
Cdd:cd19512    89 EADAFLRKRST----EKISEDLRaALNAFLYRTGE---QSNkFMLVLASNQPEQFDWAINDRID 145
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
172-303 1.76e-04

RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 42.60  E-value: 1.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 172 NRVVLLHGPPGTGKTSLCKALAQKLTIR------LSSRYRYGQLIEiNSHSL---FSKWFsESGKL-------------V 229
Cdd:COG0467    20 GSSTLLSGPPGTGKTTLALQFLAEGLRRgekglyVSFEESPEQLLR-RAESLgldLEEYI-ESGLLriidlspeelgldL 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1386813839 230 TKMFQKIQDLIDDKDALVFVlIDqveSLTAARNacrAGTEPSDAIRVVNAVLTQIdqikRHSNVVILTTSNITE 303
Cdd:COG0467    98 EELLARLREAVEEFGAKRVV-ID---SLSGLLL---ALPDPERLREFLHRLLRYL----KKRGVTTLLTSETGG 160
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
175-253 1.90e-04

Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 43.30  E-value: 1.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLT-----------------IRLSSRYRYgqLIEINSHSLFSKWFSESGKLVTKMFQKIQ 237
Cdd:COG1474    54 VLIYGPTGTGKTAVAKYVLEELEeeaeergvdvrvvyvncRQASTRYRV--LSRILEELGSGEDIPSTGLSTDELFDRLY 131

                          90
                  ....*....|....*....
gi 1386813839 238 DLIDDKDA-LVFVL--IDQ 253
Cdd:COG1474   132 EALDERDGvLVVVLdeIDY 150
ftsH CHL00176
cell division protein; Validated
 175-332 2.07e-04

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 43.50  E-value: 2.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLTIRLSSRyrygqlieinSHSLFSKWFSESGKL-VTKMFQKIQDliddkDALVFVLIDQ 253
Cdd:CHL00176  219 VLLVGPPGTGKTLLAKAIAGEAEVPFFSI----------SGSEFVEMFVGVGAArVRDLFKKAKE-----NSPCIVFIDE 283

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 254 VESLTAARNA-CRAGTEPSDaiRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVAFV--DRADIKQYIGPP---SAAAI 327
Cdd:CHL00176  284 IDAVGRQRGAgIGGGNDERE--QTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLrpGRFDRQITVSLPdreGRLDI 361


                  ....*
gi 1386813839 328 FKIYL 332
Cdd:CHL00176  362 LKVHA 366
PRK04195 PRK04195
replication factor C large subunit; Provisional
 173-193 3.13e-04

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 42.99  E-value: 3.13e-04
                          10        20
                  ....*....|....*....|.
gi 1386813839 173 RVVLLHGPPGTGKTSLCKALA 193
Cdd:PRK04195   40 KALLLYGPPGVGKTSLAHALA 60
AAA_33 pfam13671
AAA domain; This family of domains contain only a P-loop motif, that is characteriztic of the ...
 174-202 6.65e-04

AAA domain; This family of domains contain only a P-loop motif, that is characteriztic of the AAA superfamily. Many of the proteins in this family are just short fragments so there is no Walker B motif.


Pssm-ID: 463952 [Multi-domain]  Cd Length: 143  Bit Score: 39.99  E-value: 6.65e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 1386813839 174 VVLLHGPPGTGKTSLCKALAQKL-TIRLSS 202
Cdd:pfam13671   1 LILLVGLPGSGKSTLARRLLEELgAVRLSS 30
AAA_18 pfam13238
AAA domain;
175-282 1.34e-03

AAA domain;


Pssm-ID: 433052 [Multi-domain]  Cd Length: 128  Bit Score: 38.56  E-value: 1.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQkltiRLSSRYRYGQLI-EINSHSLFSKWFSESGKLVTKMFQKIQDLIDDKDALVFVLIDQ 253
Cdd:pfam13238   1 ILITGTPGVGKTTLAKELSK----RLGFGDNVRDLAlENGLVLGDDPETRESKRLDEDKLDRLLDLLEENAALEEGGNLI 76

                          90       100
                  ....*....|....*....|....*....
gi 1386813839 254 VESltaarnaCRAGTEPSDAIRVVNAVLT 282
Cdd:pfam13238  77 IDG-------HLAELEPERAKDLVGIVLR 98
cdc6 PRK00411
ORC1-type DNA replication protein;
135-254 1.44e-03

ORC1-type DNA replication protein;


Pssm-ID: 234751 [Multi-domain]  Cd Length: 394  Bit Score: 40.60  E-value: 1.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 135 LWDSLVY-DVEVKSHllDYVMTTLLFSDKNVNS------NLITWNRV--VLLHGPPGTGKTSLCKAL---AQKLTIRLSS 202
Cdd:PRK00411   11 MWDETIFkDEEVLEP--DYVPENLPHREEQIEElafalrPALRGSRPlnVLIYGPPGTGKTTTVKKVfeeLEEIAVKVVY 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 203 RY--------RYGQLIEINSHsLFSKWFSESGKLVTKMFQKIQDLIDDKDALVFVLIDQV 254
Cdd:PRK00411   89 VYincqidrtRYAIFSEIARQ-LFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDI 147
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 175-202 2.04e-03

Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein.


Pssm-ID: 398900 [Multi-domain]  Cd Length: 159  Bit Score: 38.64  E-value: 2.04e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKL--TIRLSS 202
Cdd:pfam05496  36 VLLYGPPGLGKTTLANIIANEMgvNIRITS 65
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 175-196 2.25e-03

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 40.07  E-value: 2.25e-03
                          10        20
                  ....*....|....*....|..
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKL 196
Cdd:PRK13342   39 MILWGPPGTGKTTLARIIAGAT 60
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
175-196 2.94e-03

DNA polymerase III, delta prime subunit [Replication, recombination and repair];


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 39.19  E-value: 2.94e-03
                          10        20
                  ....*....|....*....|..
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKL 196
Cdd:COG0470    21 LLLHGPPGIGKTTLALALARDL 42
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
175-193 3.00e-03

ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 40.02  E-value: 3.00e-03
                          10
                  ....*....|....*....
gi 1386813839 175 VLLHGPPGTGKTSLCKALA 193
Cdd:COG0465   178 VLLVGPPGTGKTLLAKAVA 196
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 159-300 3.06e-03

ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of photosynthesis in cyanobacteria, especially in CO2 uptake and utilization. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410915 [Multi-domain]  Cd Length: 161  Bit Score: 38.12  E-value: 3.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 159 FSDKNVNSNLITwNRVVLLHGPPGTGKTSLCKALAQKLTIrlssryrygQLIEINSHSLFSKWFSESGKLVTKMFQKIQD 238
Cdd:cd19507    19 FSKQASAYGLPT-PKGLLLVGIQGTGKSLTAKAIAGVWQL---------PLLRLDMGRLFGGLVGESESRLRQMIQTAEA 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1386813839 239 LiddkdALVFVLIDQVES-LTAARNACRAGTepsdAIRVVNAVLTQIDQikRHSNVVILTTSN 300
Cdd:cd19507    89 I-----APCVLWIDEIEKgFSNADSKGDSGT----SSRVLGTFLTWLQE--KKKPVFVVATAN 140
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 175-254 3.39e-03

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.


Pssm-ID: 459992  Cd Length: 102  Bit Score: 36.81  E-value: 3.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKLtirlssryryGQLIEINSHSLFSK------WFSESGKLVTKMFqkiqDLIDDKDALVF 248
Cdd:pfam00910   1 IWLYGPPGCGKSTLAKYLARAL----------LKKLGLPKDSVYSRnpdddfWDGYTGQPVVIID----DFGQNPDGPDE 66


                  ....*.
gi 1386813839 249 VLIDQV 254
Cdd:pfam00910  67 AELIRL 72
NadR3 COG3172
Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase ...
 173-196 5.16e-03

Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase is part of the Pathway/BioSystem: NAD biosynthesis


Pssm-ID: 442405 [Multi-domain]  Cd Length: 178  Bit Score: 37.88  E-value: 5.16e-03
                          10        20
                  ....*....|....*....|....
gi 1386813839 173 RVVLLhGPPGTGKTSLCKALAQKL 196
Cdd:COG3172    10 KIVLL-GAESTGKTTLARALAAHY 32
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 173-296 5.65e-03

AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.


Pssm-ID: 433025 [Multi-domain]  Cd Length: 167  Bit Score: 37.48  E-value: 5.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 173 RVVLLHGPPGTGKTSLCKALAQkltiRLSSRYRYGQLIEINSHSLFSKWfsesgklvTKMFQKIQDLIDDKDALVFVLID 252
Cdd:pfam13191  25 PSVLLTGEAGTGKTTLLRELLR----ALERDGGYFLRGKCDENLPYSPL--------LEALTREGLLRQLLDELESSLLE 92

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1386813839 253 QVESLTAARNACRAGTEPSDAIRVVNAVLTQIDQIKRHSNVVIL 296
Cdd:pfam13191  93 AWRAALLEALAPVPELPGDLAERLLDLLLRLLDLLARGERPLVL 136
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 175-194 5.97e-03

Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, recombination and repair];


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 38.88  E-value: 5.97e-03
                          10        20
                  ....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQ 194
Cdd:COG2256    52 MILWGPPGTGKTTLARLIAN 71
MoxR COG0714
MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway ...
 175-194 7.27e-03

MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis


Pssm-ID: 440478 [Multi-domain]  Cd Length: 292  Bit Score: 38.22  E-value: 7.27e-03
                          10        20
                  ....*....|....*....|
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQ 194
Cdd:COG0714    34 LLLEGVPGVGKTTLAKALAR 53
TIP49 pfam06068
TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and ...
 173-196 7.60e-03

TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases.


Pssm-ID: 399217 [Multi-domain]  Cd Length: 347  Bit Score: 38.44  E-value: 7.60e-03
                          10        20
                  ....*....|....*....|....
gi 1386813839 173 RVVLLHGPPGTGKTSLCKALAQKL 196
Cdd:pfam06068  51 RAVLIAGPPGTGKTALAIAISKEL 74
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
175-211 7.80e-03

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 38.19  E-value: 7.80e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1386813839 175 VLLHGPPGTGKTSLCKALAQKL--TIRLSSryryGQLIE 211
Cdd:PRK00080   54 VLLYGPPGLGKTTLANIIANEMgvNIRITS----GPALE 88
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 164-187 8.42e-03

DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438712 [Multi-domain]  Cd Length: 218  Bit Score: 37.58  E-value: 8.42e-03
                          10        20
                  ....*....|....*....|....
gi 1386813839 164 VNSNLITWNRVVLLHGPPGTGKTS 187
Cdd:cd18042     9 IASALQNSPGITLIQGPPGTGKTK 32
RecA-like_Lon cd19500
lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an ...
 174-196 8.59e-03

lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an evolutionarily conserved ATP-dependent serine protease, present in bacteria and eukaryotic mitochondria and peroxisomes, which mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Lon protease is both an ATP-dependent peptidase and a protein-activated ATPase. This RecA-like Lon domain subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410908 [Multi-domain]  Cd Length: 182  Bit Score: 37.15  E-value: 8.59e-03
                          10        20
                  ....*....|....*....|...
gi 1386813839 174 VVLLHGPPGTGKTSLCKALAQKL 196
Cdd:cd19500    39 ILCLVGPPGVGKTSLGKSIARAL 61
recomb_radB TIGR02237
DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB ...
 177-306 9.08e-03

DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).


Pssm-ID: 274047 [Multi-domain]  Cd Length: 209  Bit Score: 37.40  E-value: 9.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813839 177 LHGPPGTGKTSLCKALA------QKLTIRLS----SRYRYGQLIEINSHSLFSKW-------FSESGKLVTKMFqkiqDL 239
Cdd:TIGR02237  17 IYGPPGSGKTNICMILAvnaarqGKKVVYIDteglSPERFKQIAEDRPERALSNFivfevfdFDEQGVAIQKTS----KF 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1386813839 240 IDDKDALVFVlidqVESLTAARNACRAGtEPSDAIRVVNAVLTQIDQIKRHSNVVILTTSNITEKID 306
Cdd:TIGR02237  93 IDRDSASLVV----VDSFTALYRLELSD-DRISRNRELARQLTLLLSLARKKNLAVVITNQVYTDVN 154
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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